Thousands of refugees continued arriving in Syria from northern Lebanon on Thursday, even as the US state department warned that one of their destinations was likely to continue to be a target for US air strikes.

The planned return of at least 8,000 Syrian civilians and fighters in a deal brokered last week also marked a distinct change in Lebanese government policy toward Syrian refugees.

Until now, Lebanese prime minister Saad Hariri has said the government would only support refugee returns approved by the United Nations, but the deal this week was the result of a Hizbollah offensive around the northern Lebanese city of Arsal. That arrangement was largely negotiated between Hizbollah and the Al Qaeda-linked fighters who have been using the area as a hideout for several years.

The operation and return of the refugees appears to have raised Hizbollah’s political capital and popularity in Lebanon and Mr Hariri - a long-time opponent of the group and its role in Lebanon - found himself obliged to praise Hizbollah on Wednesday.

“What we care for is a return to normal life in Arsal and the state has performed its duties,” Mr Hariri said. “Hizbollah carried out the operation and it achieved something and what's important is the result.”

The operation appears to have rid northern Lebanon of fighters from Jabhat Fatah Al Sham, a militant group that was formally Al Qaeda’s affiliate in Syria under the name Jabhat Al Nusra. Their presence, as well of ISIL fighters, had put that part of the country beyond the control of the Lebanese government.

Estimates put the number of Syrian refugees living around Arsal at more than 40,000, many of them in camps outside the city. Fatah Al Sham’s fighters took refuge in some of those camps before Hizbollah surrounded them and negotiations began.

The refugees are being sent to Flita, a Syrian city just across the border from Arsal, and to the northern Syrian province of Idlib, which is largely controlled by Fatah Al Sham fighters, including the city of Idlib itself.

On Wednesday, Michael Ratney, the US state department’s envoy to Syria, warned that Fatah Al Sham’s presence in Idlib would result in continued US attacks. The US first bombed the militants in Idlib in 2014 and has continued to do so.

"In the event of the hegemony of Nusra Front on Idlib, it would be difficult for the United States to convince the international parties not to take the necessary military measures," Mr Ratney said, using the group’s original name and failing to specify what measures might be taken beyond the air strikes that already occur.

Human rights groups in Syria have said the US has killed civilians in previous air strikes in Idlib and other parts of northern Syria, though the US military generally claims the casualties of their air strikes are militants. Russian and Syrian planes have also bombed militants in the area.

A Syrian journalist based in Idlib said local humanitarian organisations were preparing homes for the new arrivals, but that Mr Ratney’s statement had created a fear of increased attacks from the air. “There are already always drones in the sky,” the journalist said.

Once the current transfer is completed, a separate deal could send more than 1,000 additional refugees back to Syria from eastern Lebanon’s Bekaa Valley as early as Friday. That deal was brokered between the Syrian government and a local leader from the Syrian town of Arsal Al Ward who lives in Lebanon, although sources familiar with the negotiations said Hizbollah was also involved.

In some respects, the deals resemble recent arrangements in Syria that saw fighters and civilians being bussed from one part of Syria to another under locally brokered ceasefires between the Syrian government and rebel groups. Some of those transfers, also outside the purview of the UN, have been criticised as forced displacement based on sectarian affiliations.

“Refugee returns need to be an individual decision, and this decision should be made free from any undue pressure,” said Lisa Abou Khaled, the spokeswoman for the UN High Commissioner for Refugees in Lebanon. “We would be concerned about them understanding the conditions they are returning to.”